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Course Papers

  • Hierarchical Models Weinberger and Warren et al. 2020 1 (view paper)
  • Serotype Replacement Weinberger and Warren et al. 2018 2 (view paper)
  • Correlates of Nonrandom Patterns of Serotype Switching in Pneumococcus Joshi and Al-Mamun et al. 2020 3 (view paper)
  • 2022 Annual Epidemiological Report for Invasive Pneumococcal Disease (IPD) 4 (view paper)

Lecture Slides

Codespaces

Weekly Modules

Please download the codespaces provided for each weekly module release. Note that you may need to adjust the filepath for some references inside the code. It is recommended that you use the starter codespace package, which includes the following:

  • An Rproj file to set your root directory.
  • An renv lockfile.
  • A suggested .gitignore.
  • A README.md file with directions for using the codespace and guidelines for adding the code to your own GitHub remote repository.

Subsequent weekly releases should be placed inside your root project directory. For instance, if you are using the directory “~/bdsy-phm-individual”, place the weekly releases within that directory.

Project Datasets and Materials

Each group will be assigned data from one of three countries: Malawi, Nepal, or Peru. The datasets include the incidence of pneumococcal-caused respiratory disease, or in some cases, any causes of pneumonia, along with Global Pneumococcal Sequencing Project (GPS) sequencing data. Below, you will find these datasets, the source documentation or papers from which they were obtained, and any ancillary documentation such as a Data Dictionary.

Note

Not all sources provided a Data Dictionary, so students will need to explain their variables using the context provided by the source documentation.

Find the raw incidents data, GPS data, and literature papers 8.

Find the raw incidents data, GPS data, and literature papers 9,10.

Find the raw incidents data, GPS data, and data dictionary 11.

  • Peru Epidemiological surveillance of Acute Respiratory Infections (ARI) Data Page (link to page)

Templates

Tips and Advice

Research Like a Pro

It is vital that you keep track of and disclose all the references you use to support your research. There are many tools available to help you with this, so discuss with your team and decide on a preferred method for reference tracking.

In my research, I use Mendeley, which comes with a Web Importer plug-in that makes it easy to compile different types of references. It conveniently formats these entries to various styles, including LaTeX and BibTeX.

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References

1.
Warren, J. L. & Weinberger, D. M. Estimating serotype-specific efficacy of pneumococcal conjugate vaccines using hierarchical models. Epidemiology 31, 259–262 (2020).
2.
Weinberger, D. M. et al. Differences in the impact of pneumococcal serotype replacement in individuals with and without underlying medical conditions. Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America 69, 100 (2018).
3.
Joshi, S. S., Al-Mamun, M. A. & Weinberger, D. M. Correlates of nonrandom patterns of serotype switching in pneumococcus. The Journal of Infectious Diseases 221, 1669–1676 (2020).
4.
Disease Prevention, E. C. for & Control. Invasive pneumococcal disease - annual epidemiological report for 2022. Annual Epidemiological Report (2025).
5.
Project, G. P. S. & Institute, S. Global pneumococcal sequencing (GPS) project.
6.
Project, G. P. S. & Institute, S. Monocle data viewer. GPS release 6.0.
7.
Project, G. P. S. & Institute, S. GPS database dictionary.
8.
Bar-Zeev, N. et al. Impact and effectiveness of 13-valent pneumococcal conjugate vaccine on population incidence of vaccine and non-vaccine serotype invasive pneumococcal disease in blantyre, malawi, 2006–18: Prospective observational time-series and case-control studies. The Lancet Global Health 9, e989–e998 (2021).
9.
Kandasamy, R. et al. Decline in pneumococcal vaccine serotype carriage, multiple-serotype carriage, and carriage density in nepalese children after PCV10 introduction: A pre-post comparison study. Vaccine 42, 4066–4071 (2024).
10.
Kandasamy, R. et al. Multi-serotype pneumococcal nasopharyngeal carriage prevalence in vaccine naïve nepalese children, assessed using molecular serotyping. PLOS ONE 10, e0114286 (2015).
11.
Gobierno Digital Presidencia del Consejo de Ministros, S. de. Vigilancia epidemiologica de infecciones respiratoiras agudas (IRA) | plataforma nacional de datos abiertos. (2024).